Process fish surveys

library(ggtext)
library(paletteer)
library(sf)
library(terra)
library(tidyverse)
library(gt)
library(DBI)
library(bigrquery)

knitr::opts_chunk$set(eval = T, warning = F, message = F, include = T, echo = F)

PristineSeasR::set_ps_paths(email = "marine.data.science@ngs.org")

exp_path <- file.path(ps_science_path, "expeditions", "Niue-2023")

ps_data_path <- file.path(ps_science_path, "datasets/")

bq_auth(email = "marine.data.science@ngs.org")

bq_connection <- dbConnect(bigquery(), 
                           project = "pristine-seas")

1 Metadata

Number of stations per region, habitat, and exposure
habitat	exposure	n_stations	n_strata	n_transects
Antiope
Forereef	Windward	2	1	12
Beveridge
Backreef	Lagoon	5	1	20
Forereef	Leeward	5	2	30
Forereef	Windward	7	2	42
Niue
Forereef	Leeward	13	2	64

2 Data processsing

2.1 Observations

2.2 Clean taxa

2.3 Calculate biomass

2.4 DB Upload

3 Analyses

3.1 By location

Number of workstations and average species richness (# species/station-strata), fish abundance (ind/m2), and biomass (g/m2) for each location
location	stations	transects	n_taxa	ind_m2	gr_m2
Antiope	2	12	17.00	0.47	36.97
Beveridge	17	92	37.12	2.16	270.94
Niue	13	64	41.35	2.18	75.56

3.2 By depth strata

Number of workstations and average species richness (# species/station-strata), fish abundance (ind/m2), and biomass (g/m2) for each location and depth strata
Location/Strata	stations	transects	n_taxa	ind_m2	gr_m2
Antiope
Shallow	2	12	17.00	0.47	36.97
Beveridge
Deep	12	36	42.67	2.10	256.58
Shallow	12	36	37.33	2.28	183.87
Supershallow	5	20	30.20	2.10	392.66
Niue
Deep	13	32	40.62	2.09	71.97
Shallow	13	32	42.08	2.27	79.16

3.3 By exposure

Number of workstations and average species richness (# species/station-strata), fish abundance (ind/m2), and biomass (g/m2) for each location and exposure
Location/Strata	stations	transects	n_taxa	ind_m2	gr_m2
Antiope
Windward	2	12	17.00	0.47	36.97
Beveridge
Lagoon	5	20	30.20	2.10	392.66
Leeward	5	30	39.60	2.33	154.53
Windward	7	42	40.29	2.09	267.15
Niue
Leeward	13	64	41.35	2.18	75.56

3.4 By habitat

Number of workstations and average species richness (# species/station-strata), fish abundance (ind/m2), and biomass (g/m2) for each location and habitat
Location/Strata	stations	transects	n_taxa	ind_m2	gr_m2
Antiope
Forereef	2	12	17.00	0.47	36.97
Beveridge
Backreef	5	20	30.20	2.10	392.66
Forereef	12	72	40.00	2.19	220.23
Niue
Forereef	13	64	41.35	2.18	75.56

3.5 Univariate adonis

Results of Adonis model for univariate analysis of fish species richness
	df	SumOfSqs	R2	statistic	p.value
depth_strata	1	40.500	0.006	0.636	0.463
location	2	1489.737	0.230	11.688	0.001
exposure	1	2.743	0.000	0.043	0.828
habitat	0	0.000	0.000	Inf	NA
Residual	58	3696.242	0.570	NA	NA
Total	63	6487.609	1.000	NA	NA

Results of Adonis model for univariate analysis of fish abundance
	df	SumOfSqs	R2	statistic	p.value
depth_strata	1	0.396	0.007	0.516	0.483
location	2	8.688	0.155	5.657	0.005
exposure	1	0.335	0.006	0.436	0.507
habitat	0	0.000	0.000	Inf	NA
Residual	58	44.542	0.793	NA	NA
Total	63	56.151	1.000	NA	NA

Results of Adonis model for univariate analysis of fish biomass
	df	SumOfSqs	R2	statistic	p.value
depth_strata	1	12138.26	0.004	0.392	0.541
location	2	179920.08	0.066	2.909	0.069
exposure	1	73987.53	0.027	2.392	0.126
habitat	0	0.00	0.000	Inf	NA
Residual	58	1793727.50	0.656	NA	NA
Total	63	2735734.88	1.000	NA	NA

3.6 By family

Number of families, species, total abundance (ind/m2) and biomass (g/m2) by taxonmic order
Class/Order	family	n_genus	n_species	total_abundance	total_biomass
Teleostei
Acanthuriformes	Acanthuridae	4	25	0.358	45.617
Eupercaria incertae sedis	Scaridae	4	10	0.023	24.665
Centrarchiformes	Kyphosidae	1	1	0.022	17.496
Perciformes	Serranidae	8	12	0.128	7.412
Eupercaria incertae sedis	Lutjanidae	4	5	0.014	7.295
Mulliformes	Mullidae	2	6	0.029	6.348
Carangiformes	Carangidae	4	6	0.005	5.318
Tetraodontiformes	Balistidae	5	8	0.021	4.751
Eupercaria incertae sedis	Labridae	18	33	0.208	4.559
Eupercaria incertae sedis	Lethrinidae	2	2	0.007	4.213
Ovalentaria incertae sedis	Pomacentridae	9	21	0.986	3.505
Holocentriformes	Holocentridae	3	4	0.014	3.256
Acanthuriformes	Chaetodontidae	3	17	0.058	2.915
Carangaria incertae sedis	Sphyraenidae	1	2	0.002	2.306
Acanthuriformes	Pomacanthidae	3	6	0.067	1.400
Centrarchiformes	Cirrhitidae	4	6	0.078	0.873
Syngnathiformes	Fistulariidae	1	1	0.000	0.397
Tetraodontiformes	Monacanthidae	1	2	0.000	0.358
Eupercaria incertae sedis	Haemulidae	1	1	0.000	0.304
Acanthuriformes	Zanclidae	1	1	0.002	0.302
Anguilliformes	Muraenidae	1	2	0.000	0.243
Tetraodontiformes	Tetraodontidae	2	2	0.001	0.148
Perciformes	Pinguipedidae	1	3	0.002	0.104
Perciformes	Scorpaenidae	1	2	0.000	0.058
Tetraodontiformes	Diodontidae	1	1	0.000	0.034
Gobiiformes	Microdesmidae	2	2	0.025	0.030
Blenniiformes	Blenniidae	2	3	0.013	0.023
Aulopiformes	Synodontidae	1	1	0.000	0.020
Kurtiformes	Apogonidae	1	1	0.001	0.008
Elasmobranchii
Carcharhiniformes	Carcharhinidae	2	2	0.001	32.987

3.7 By trophic group

3.8 By species

Fish abundance (ind/m2), biomass (g/m2), and frequency of observation (% strata)

3.9 Community composition

Results of community composition adonis model
term	df	SumOfSqs	R2	statistic	p.value
location	2	2.327	0.102	4.279	0.001
exposure	1	1.305	0.057	4.800	0.001
habitat	0	0.000	0.000	Inf	NA
depth_strata	1	0.563	0.025	2.070	0.012
Residual	58	15.769	0.689	NA	NA
Total	63	22.900	1.000	NA	NA

Overall fit of the ordination model
term	df	SumOfSqs	statistic	p.value
Model	4	6.924	4.735	0.001
Residual	59	21.567	NA	NA

Significance of each axis in the ordination model
term	df	SumOfSqs	statistic	p.value
dbRDA1	1	3.058	8.365	0.001
dbRDA2	1	1.811	4.954	0.001
dbRDA3	1	1.372	3.753	0.001
dbRDA4	1	0.683	1.870	0.001
Residual	59	21.567	NA	NA

Significace of each term in the ordination model
term	df	SumOfSqs	statistic	p.value
location	2	3.805	5.205	0.001
exposure	2	3.119	4.266	0.001
Residual	59	21.567	NA	NA

3.10 Changes since 2016

Changes in fish biomass by location and depth strata (2016-2023)
Location/Strata	2016	2023
Beveridge
Deep	162.77	256.58
Shallow	95.90	183.87
Supershallow	74.94	392.66
Niue
Deep	46.03	71.97
Shallow	62.89	79.16
Supershallow	78.62	NA

Results of Adonis model for univariate analysis of fish diversity
term	df	SumOfSqs	R2	statistic	p.value
depth_strata	2	48508.018	0.014	1.424	0.250
habitat	1	1322.878	0.000	0.078	0.767
location	2	339187.897	0.100	9.960	0.007
year	1	282385.038	0.083	16.585	0.001
Residual	144	2451879.323	0.724	NA	NA
Total	150	3387213.191	1.000	NA	NA